Harikrishna Nakshatri

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https://hdl.handle.net/1805/17677

Enhancing Hormone Therapy and Chemotherapy Sensitivity of Breast Cancer

Breast cancers are broadly classified into estrogen receptor positive (ER+) and estrogen receptor negative (ER-) subtypes. Anti-estrogens (hormone therapy) and chemotherapy are treatment options for ER+ and ER- breast cancers, respectively. However, resistance to therapies is very common, and disease recurrence is associated with the spread of the diseases to multiple organs (metastasis). Dr. Nakshatri's research lab focuses on mechanisms of resistance to anti-estrogens and chemotherapy, predicting therapy resistance at the time of diagnosis, and developing effective combination therapies, particularly for metastasis.

His group has identified and commercialized biomarkers that may predict response to anti-estrogens, demonstrating that a protein complex min a subset of breast cancer plays a role in chemotherapy resistance and metastasis-research that, in collaboration with other institutions, is currently in phase I clinical trial. Additional work included circulating biomarkers that predict the effect of breast cancer on the general well-being of a patient and a new patent application on how to treat specific subtypes of breast cancer. His group also established a culturing method to grow and genomically characterize primary tumors and metastasis at the individual level.

Dr. Nakshatri's work to identify biomarkers of disease progression is another example of how IUPUI faculty are TRANSLATING RESEARCH INTO PRACTICE.

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Now showing 1 - 10 of 22

AKT Alters Genome-Wide Estrogen Receptor α Binding and Impacts Estrogen Signaling in Breast Cancer
(American Society for Microbiology, 2008-12) Bhat-Nakshatri, Poornima; Wang, Guohua; Appaiah, Hitesh; Luktuke, Nikhil; Carroll, Jason S.; Geistlinger, Tim R.; Brown, Myles; Badve, Sunil; Liu, Yunlong; Nakshatri, Harikrishna
Estrogen regulates several biological processes through estrogen receptor α (ERα) and ERβ. ERα-estrogen signaling is additionally controlled by extracellular signal activated kinases such as AKT. In this study, we analyzed the effect of AKT on genome-wide ERα binding in MCF-7 breast cancer cells. Parental and AKT-overexpressing cells displayed 4,349 and 4,359 ERα binding sites, respectively, with ∼60% overlap. In both cell types, ∼40% of estrogen-regulated genes associate with ERα binding sites; a similar percentage of estrogen-regulated genes are differentially expressed in two cell types. Based on pathway analysis, these differentially estrogen-regulated genes are linked to transforming growth factor β (TGF-β), NF-κB, and E2F pathways. Consistent with this, the two cell types responded differently to TGF-β treatment: parental cells, but not AKT-overexpressing cells, required estrogen to overcome growth inhibition. Combining the ERα DNA-binding pattern with gene expression data from primary tumors revealed specific effects of AKT on ERα binding and estrogen-regulated expression of genes that define prognostic subgroups and tamoxifen sensitivity of ERα-positive breast cancer. These results suggest a unique role of AKT in modulating estrogen signaling in ERα-positive breast cancers and highlights how extracellular signal activated kinases can change the landscape of transcription factor binding to the genome.
Estradiol-regulated microRNAs control estradiol response in breast cancer cells
(Oxford University Press, 2009-08) Bhat-Nakshatri, Poornima; Wang, Guohua; Collins, Nikail R.; Thomson, Michael J.; Geistlinger, Tim R.; Carroll, Jason S.; Brown, Myles; Hammond, Scott; Srour, Edward F.; Liu, Yunlong; Nakshatri, Harikrishna
Estradiol (E2) regulates gene expression at the transcriptional level by functioning as a ligand for estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ). E2-inducible proteins c-Myc and E2Fs are required for optimal ERα activity and secondary estrogen responses, respectively. We show that E2 induces 21 microRNAs and represses seven microRNAs in MCF-7 breast cancer cells; these microRNAs have the potential to control 420 E2-regulated and 757 non-E2-regulated mRNAs at the post-transcriptional level. The serine/threonine kinase, AKT, alters E2-regulated expression of microRNAs. E2 induced the expression of eight Let-7 family members, miR-98 and miR-21 microRNAs; these microRNAs reduced the levels of c-Myc and E2F2 proteins. Dicer, a ribonuclease III enzyme required for microRNA processing, is also an E2-inducible gene. Several E2-regulated microRNA genes are associated with ERα-binding sites or located in the intragenic region of estrogen-regulated genes. We propose that the clinical course of ERα-positive breast cancers is dependent on the balance between E2-regulated tumor-suppressor microRNAs and oncogenic microRNAs. Additionally, our studies reveal a negative-regulatory loop controlling E2 response through microRNAs as well as differences in E2-induced transcriptome and proteome.
Subcellular Localization of Activated AKT in Estrogen Receptor- and Progesterone Receptor-Expressing Breast Cancers
(Elsevier, 2010-05) Badve, Sunil; Collins, Nikail R.; Bhat-Nakshatri, Poornima; Turbin, Dmitry; Leung, Samuel; Thorat, Mangesh; Dunn, Sandra E.; Geistlinger, Tim R.; Carroll, Jason S.; Brown, Myles; Bose, Shikha; Teitell, Michael A.; Nakshatri, Harikrishna
Activated v-AKT murine thymoma viral oncogene homolog 1 (AKT)/protein kinase B (PKB) kinase (pAKT) is localized to the plasma membrane, cytoplasm, and/or nucleus in 50% of cancers. The clinical importance of pAKT localization and the mechanism(s) controlling this compartmentalization are unknown. In this study, we examined nuclear and cytoplasmic phospho-AKT (pAKT) expression by immunohistochemistry in a breast cancer tissue microarray (n = 377) with ≈15 years follow-up and integrated these data with the expression of estrogen receptor (ER)α, progesterone receptor (PR), and FOXA1. Nuclear localization of pAKT (nuclear-pAKT) was associated with long-term survival (P = 0.004). Within the ERα+/PR+ subgroup, patients with nuclear-pAKT positivity had better survival than nuclear-pAKT–negative patients (P ≤ 0.05). The association of nuclear-pAKT with the ERα+/PR+ subgroup was validated in an independent cohort (n = 145). TCL1 family proteins regulate nuclear transport and/or activation of AKT. TCL1B is overexpressed in ERα-positive compared with ERα-negative breast cancers and in lung metastasis–free breast cancers. Therefore, we examined the possible control of TCL1 family member(s) expression by the estrogen:ERα pathway. Estradiol increased TCL1B expression and increased nuclear-pAKT levels in breast cancer cells; short- interfering RNA against TCL1B reduced nuclear-pAKT. Overexpression of nuclear-targeted AKT1 in MCF-7 cells increased cell proliferation without compromising sensitivity to the anti-estrogen, tamoxifen. These results suggest that subcellular localization of activated AKT plays a significant role in determining its function in breast cancer, which in part is dependent on TCL1B expression.
Prognosis of hormone-dependent breast cancers: implications of the presence of dysfunctional transcriptional networks activated by insulin via the immune transcription factor T-bet
(American Association for Cancer Research, 2010-01-15) McCune, Kasi; Bhat-Nakshatri, Poornima; Thorat, Mangesh A; Nephew, Kenneth P; Badve, Sunil; Nakshatri, Harikrishna
Estrogen receptor alpha (ERα)-positive breast cancers that co-express trans cription factors GATA-3 and FOXA1 have a favorable prognosis. These transcription factors form an autoregulatory hormonal network that influences estrogen responsiveness and sensitivity to hormonal therapy. Disruption of this network may be a mechanism whereby ERα positive breast cancers become resistant to therapy. The transcription factor T-bet is a negative regulator of GATA-3 in the immune system. In this study, we report that insulin increases the expression of T-bet in breast cancer cells, which correlates with reduced expression of GATA-3, FOXA1 and the ERα:FOXA1:GATA-3 target gene GREB-1. The effects of insulin on GATA-3 and FOXA1 could be recapitulated through overexpression of T-bet in MCF-7 cells (MCF-7-T-bet). Chromatin immunoprecipitation assays revealed reduced ERα binding to GREB-1 enhancer regions in MCF-7-T-bet cells and in insulin treated MCF-7 cells. MCF-7-T-bet cells were resistant to tamoxifen in the presence of insulin and displayed prolonged ERK and AKT activation in response to epidermal growth factor treatment. ERα-positive cells with intrinsic tamoxifen resistance as well as MCF-7 cells with acquired tamoxifen and fulvestrant resistance expressed elevated levels of T-bet and/or reduced levels of FOXA1 and GATA-3. Analysis of publicly available databases revealed ERα-positive/T-bet-positive breast cancers expressing lower levels of FOXA1 (p=0.0137) and GATA-3 (p=0.0063) compared to ERα-positive/T-bet-negative breast cancers. Thus, T-bet expression in primary tumors and circulating insulin levels may serve as surrogate biomarkers to identify ERα-positive breast cancers with a dysfunctional hormonal network, enhanced growth factor signaling, and resistance to hormonal therapy.
Radiation resistance in breast cancer: are CD44+/CD24-/proteosomelow/PKH26+ cells to blame?
(BMC, 2010) Nakshatri, Harikrishna
Identification and characterization of cancer-initiating cells (CICs) enriched for stem cell-like functions and the establishment of a link between CICs and tumor recurrence, chemotherapy resistance and radiation resistance, and metastasis have been the focus of cancer research for the last eight years. Although this field has its share of controversies, it is becoming apparent that cells isolated from recurrent or residual tumors or both are enriched for cancer cells that have a specific phenotype compared with heterogeneous cells in the primary tumor. Enrichment of CICs in tumors subjected to radiation therapy could be due in part to the delivery of sublethal doses of treatment and the efficient radical scavenging system within CICs. Sublethal doses of radiation are sufficient to induce senescence of non-CICs while forcing CICs to gain several new properties related to cell cycle progression in addition to maintaining or enhancing stem cell characteristics of pre-treatment CICs. Characterizing pathways responsible for the increase in CICs after therapy and exploiting the unique characteristics of therapy-resistant CICs for developing targeted therapies are becoming a central focus of research in the rapidly evolving field of CICs.
ANTXR1, a stem cell enriched functional biomarker, connects collagen signaling to cancer stem-like cells and metastasis in breast cancer
(American Association for Cancer Research, 2013-09-15) Chen, Daohong; Bhat-Nakshatri, Poornima; Goswami, Chirayu; Badve, Sunil; Nakshatri, Harikrishna
Cancer stem-like cells are thought to contribute to tumor recurrence. The anthrax toxin receptor ANTXR1 has been identified as a functional biomarker of normal stem cells and breast cancer stem-like cells. Primary stem cell-enriched basal cells (CD49f+/EpCAM−/Lin−) expressed higher levels of ANTXR1 compared to mature luminal cells. CD49f+/EpCAM−, CD44+/EpCAM−, CD44+/CD24− or ALDEFLUOR-positive subpopulations of breast cancer cells were enriched for ANTXR1 expression. CD44+/CD24−/ANTXR1+ cells displayed enhanced self-renewal as measured by mammosphere assay compared to CD44+/CD24−/ANTXR1− cells. Activation of ANTXR1 by its natural ligand C5A, a fragment of collagen VI α3, increased stem cell self-renewal in mammosphere assays and Wnt signaling including the expression of the Wnt receptor LRP6, phosphorylation of GSK3α/β and elevated expression of Wnt target genes. RNAi-mediated silencing of ANTXR1 enhanced the expression of luminal-enriched genes but diminished Wnt signaling including reduced LRP6 and ZEB1 expression, self-renewal, invasion, tumorigenicity and metastasis. ANTXR1 silencing also reduced the expression of HSPA1A, which is overexpressed in metastatic breast cancer stem cells. Analysis of public databases revealed ANTXR1 amplification in medullary breast carcinoma and overexpression in estrogen receptor-negative breast cancers with the worst outcome. Further, ANTXR1 is among the 10% most overexpressed genes in breast cancer and is co-expressed with collagen VI. Thus, ANTXR1:C5A interactions bridge a network of collagen cleavage and remodeling in the tumor microenvironment, linking it to a stemness signaling network drives metastatic progression.
PROGgene: gene expression based survival analysis web application for multiple cancers
(Springer, 2013-10-28) Goswami, Chirayu Pankaj; Nakshatri, Harikrishna
Background Identification of prognostic mRNA biomarkers has been done for various cancer types. The data that are published from such studies are archived in public repositories. There are hundreds of such datasets available for multiple cancer types in public repositories. Wealth of such data can be utilized to study prognostic implications of mRNA in different cancers as well as in different populations or subtypes of same cancer. Description We have created a web application that can be used for studying prognostic implications of mRNA biomarkers in a variety of cancers. We have compiled data from public repositories such as GEO, EBI Array Express and The Cancer Genome Atlas for creating this tool. With 64 patient series from 18 cancer types in our database, this tool provides the most comprehensive resource available for survival analysis to date. The tool is called PROGgene and it is available at http://www.compbio.iupui.edu/proggene. Conclusions We present this tool as a hypothesis generation tool for researchers to identify potential prognostic mRNA biomarkers to follow up with further research. For this reason, we have kept the web application very simple and straightforward. We believe this tool will be useful in accelerating biomarker discovery in cancer and quickly providing results that may indicate disease-specific prognostic value of specific biomarkers.
Identification of FDA-approved Drugs Targeting Breast Cancer Stem Cells Along With Biomarkers of Sensitivity
(Nature Research, 2013-08-28) Bhat-Nakshatri, Poornima; Goswami, Chirayu P.; Badve, Sunil; Sledge, George W.; Nakshatri, Harikrishna
Recently developed genomics-based tools are allowing repositioning of Food and Drug Administration (FDA)-approved drugs as cancer treatments, which were employed to identify drugs that target cancer stem cells (CSCs) of breast cancer. Gene expression datasets of CSCs from six studies were subjected to connectivity map to identify drugs that may ameliorate gene expression patterns unique to CSCs. All-trans retinoic acid (ATRA) was negatively connected with gene expression in CSCs. ATRA reduced mammosphere-forming ability of a subset of breast cancer cells, which correlated with induction of apoptosis, reduced expression of SOX2 but elevated expression of its antagonist CDX2. SOX2/CDX2 ratio had prognostic relevance in CSC-enriched breast cancers. K-ras mutant breast cancer cell line enriched for CSCs was resistant to ATRA, which was reversed by MAP kinase inhibitors. Thus, ATRA alone or in combination can be tested for efficacy using SOX2, CDX2, and K-ras mutation/MAPK activation status as biomarkers of response.
A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry
(IEEE, 2017-11) Yang, Runmin; Zhu, Daming; Kou, Qiang; Bhat-Nakshatri, Poomima; Nakshatri, Harikrishna; Wu, Si; Liu, Xiaowen; BioHealth Informatics, School of Informatics and Computing
Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. However, it is extremely slow to align a query spectrum against all protein sequences in a large database when the target proteoform that produced the spectrum contains post-translational modifications and/or mutations. As a result, efficient and sensitive protein sequence filtering algorithms are essential for speeding up database search. In this paper, we propose a novel filtering algorithm, which generates spectrum graphs from subspectra of the query spectrum and searches them against the protein database to find good candidates. Compared with the sequence tag and gaped tag approaches, the proposed method circumvents the step of tag extraction, thus simplifying data processing. Experimental results on real data showed that the proposed method achieved both high speed and high sensitivity in protein sequence filtration.
Inflammation-associated microRNA changes in circulating exosomes of heart failure patients
(BMC, 2017-12-19) Beg, Faheemullah; Wang, Ruizhong; Saeed, Zeb; Devaraj, Srikant; Masoor, Kamalesh; Nakshatri, Harikrishna; Surgery, School of Medicine
Objective MiR-486 and miR-146a are cardiomyocyte-enriched microRNAs that control cell survival and self-regulation of inflammation. These microRNAs are released into circulation and are detected in plasma or in circulating exosomes. Little is known whether heart failure affects their release into circulation, which this study investigated. Results Total and exosome-specific microRNAs in plasma of 40 heart failure patients and 20 controls were prepared using the miRVana Kit. We measured exosomal and total plasma microRNAs separately because exosomes serve as cargos that transfer biological materials and alter signaling in distant organs, whereas microRNAs in plasma indicate the level of tissue damage and are mostly derived from dead cells. qRT-PCR was used to quantify miR-486, miR-146a, and miR-16. Heart failure did not significantly affect plasma miR-486/miR-16 and miR-146a/miR-16 ratio, although miR-146a/miR-16 showed a trend of elevated expression (2.3 ± 0.79, p = 0.27). By contrast, circulating exosomal miR-146a/miR-16 ratio was higher in heart failure patients (2.46 ± 0.51, p = 0.05). miR-146a is induced in response to inflammation as a part of inflammation attenuation circuitry. Indeed, Tnfα and Gm-csf increased miR-146a but not miR-486 in the cardiomyocyte cell line H9C2. These results, if confirmed in a larger study, may help to develop circulating exosomal miR-146a as a biomarker of heart failure.

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